Merge branch 'master' into dev-poly

* master:
  update petsc reader with new dimension syntax
  use keyword for name argument in doctests
  tweaks to geometry modifications
  Update I/O routines to reflect new Dimension initialization syntax.
  Update I/O routines to reflect new Dimension initialization syntax.

src/petclaw/io/petsc.py

@@ -176,7 +176,7 @@ def read(solution,frame,path='./',file_prefix='claw',read_aux=False,options={}):
         dimensions = []
         for i in xrange(num_dim):
             dimensions.append(
-                petclaw.Dimension(names[i],lower[i],lower[i] + n[i]*d[i],n[i]))
+                petclaw.Dimension(lower[i],lower[i] + n[i]*d[i],n[i],name=names[i]))
         patch = petclaw.Patch(dimensions)
         patch.level = level 
         state = petclaw.State(patch,num_eqn,num_aux)

src/pyclaw/geometry.py

@@ -49,8 +49,8 @@ class Grid(object):
     A PyClaw grid is usually constructed from a tuple of PyClaw Dimension objects:
 
         >>> from clawpack.pyclaw.geometry import Dimension, Grid      
-        >>> x = Dimension('x',0.,1.,10)
-        >>> y = Dimension('y',-1.,1.,25)
+        >>> x = Dimension(0.,1.,10,name='x')
+        >>> y = Dimension(-1.,1.,25,name='y')
         >>> grid = Grid((x,y))
         >>> print grid
         2-dimensional domain (x,y)
@@ -71,7 +71,7 @@ class Grid(object):
 
     A grid can be extended to higher dimensions using the add_dimension() method:
 
-        >>> z=Dimension('z',-2.0,2.0,21)
+        >>> z=Dimension(-2.0,2.0,21,name='z')
         >>> grid.add_dimension(z)
         >>> grid.num_dim
         3
@@ -83,11 +83,13 @@ class Grid(object):
     We can get the x, y, and z-coordinate arrays of cell edges and centers from the grid.
     Properties beginning with 'c' refer to the computational (unmapped) domain, while
     properties beginning with 'p' refer to the physical (mapped) domain.  For grids with
-    no mapping, the two are identical.  Notice also the difference between 'center' and
-    'centers':
+    no mapping, the two are identical.  Also note the difference between 'center' and
+    'centers'.
 
-        >>> grid.p_center([1,2,3])
-        [0.15000000000000002, -0.80000000000000004, -1.3333333333333335]
+        >>> import numpy as np
+        >>> np.set_printoptions(precision=2)  # avoid doctest issues with roundoff
+        >>> grid.c_center([1,2,3])
+        array([ 0.15, -0.8 , -1.33])
         >>> grid.p_edges[0][0,0,0]
         0.0
         >>> grid.p_edges[1][0,0,0]
@@ -97,7 +99,7 @@ class Grid(object):
 
     It's also possible to get coordinates for ghost cell arrays:
 
-        >>> x = Dimension('x',0.,1.,5)
+        >>> x = Dimension(0.,1.,5,name='x')
         >>> grid1d = Grid([x])
         >>> grid1d.c_centers
         [array([ 0.1,  0.3,  0.5,  0.7,  0.9])]
@@ -110,7 +112,7 @@ class Grid(object):
     or to adjust the local spacing of grid cells.  For instance, we can
     use smaller cells on the left and larger cells on the right by doing:
 
-        >>> double = lambda x : x[0]**2
+        >>> double = lambda xarr : np.array([x**2 for x in xarr])
         >>> grid1d.mapc2p = double
         >>> grid1d.p_centers
         array([ 0.01,  0.09,  0.25,  0.49,  0.81])
@@ -222,8 +224,6 @@ def __init__(self,dimensions):
         for dim in dimensions:
             self.add_dimension(dim)
 
-        self.mapc2p = identity_map[str(self.num_dim)]
-
         super(Grid,self).__init__()
 
     def _clear_cached_values(self):
@@ -250,6 +250,8 @@ def add_dimension(self,dimension):
         self._dimensions.append(dimension.name)
         setattr(self,dimension.name,dimension)
         self._clear_cached_values()
+        # Reset mapping as it presumably makes no sense now
+        self.mapc2p = identity_map[str(self.num_dim)]
 
 
     def get_dim_attribute(self,attr):
@@ -264,7 +266,7 @@ def __copy__(self):
     def __str__(self):
         output = "%s-dimensional domain " % str(self.num_dim)
         output += "("+",".join([dim.name for dim in self.dimensions])+")\n"
-        if self.mapc2p == identity_map:
+        if self.mapc2p in identity_map.values():
             output += "No mapping\n"
             output += "Extent:  "
         else:
@@ -331,7 +333,7 @@ def c_center(self,ind):
         r"""Compute center of computational cell with index ind."""
 
         index = [np.array(i) for i in ind]
-        return [self.c_centers[i][index] for i in range(self.num_dim)]
+        return np.array([self.c_centers[i][index] for i in range(self.num_dim)])
 
     def p_center(self,ind):
         r"""Compute center of physical cell with index ind."""

src/pyclaw/io/ascii.py

@@ -225,7 +225,8 @@ def read(solution,frame,path='./',file_prefix='fort',read_aux=False,
         names = ['x','y','z']
         import clawpack.pyclaw as pyclaw
         Dim = pyclaw.Dimension
-        dimensions = [Dim(names[i],lower[i],lower[i] + n[i]*d[i],n[i]) for i in xrange(num_dim)]
+        dimensions = [Dim(lower[i],lower[i] + n[i]*d[i],n[i],name=names[i]) \
+                for i in xrange(num_dim)]
         patch = pyclaw.geometry.Patch(dimensions)
         state= pyclaw.state.State(patch,num_eqn,num_aux)
         state.t = t

src/pyclaw/io/binary.py

@@ -97,7 +97,7 @@ def read(solution,frame,path='./',file_prefix='fort',read_aux=False,
         dimensions = []
         for i in xrange(num_dim):
             dimensions.append(
-                pyclaw.geometry.Dimension(names[i],lower[i],lower[i] + n[i]*d[i],n[i]))
+                pyclaw.geometry.Dimension(lower[i],lower[i] + n[i]*d[i],n[i]),name=names[i])
         patch = pyclaw.geometry.Patch(dimensions)
         state= pyclaw.state.State(patch,num_eqn,num_aux)
         state.t = t

src/pyclaw/io/hdf5.py

@@ -210,10 +210,11 @@ def read(solution,frame,path='./',file_prefix='claw',read_aux=True,
             dim_names = patch.attrs['dimensions']
             for dim_name in dim_names:
                 # Create dimension
-                dim = pyclaw.solution.Dimension(dim_name,
+                dim = pyclaw.solution.Dimension(
                                     patch.attrs["%s.lower" % dim_name],
                                     patch.attrs["%s.upper" % dim_name],
-                                    patch.attrs["%s.num_cells" % dim_name])                    
+                                    patch.attrs["%s.num_cells" % dim_name],
+                                    name = dim_name)
                 # Optional attributes
                 for attr in ['bc_lower','bc_upper','units']:
                     attr_name = "%s.%s" % (dim_name,attr)

src/pyclaw/io/netcdf.py

@@ -280,10 +280,11 @@ def read(solution,frame,path='./',file_prefix='claw',read_aux=True,
             # Read in dimension attribute to keep dimension order
             dim_names = getattr(subgroup,'dim_names')
             for dim_name in dim_names:
-                dim = pyclaw.solution.Dimension(dim_name, 
+                dim = pyclaw.solution.Dimension(
                                       getattr(subgroup,'%s.lower' % dim_name),
                                       getattr(subgroup,'%s.upper' % dim_name),
-                                      getattr(subgroup,'%s.n' % dim_name))
+                                      getattr(subgroup,'%s.n' % dim_name),
+                                      name = dim_name)
                  # Optional attributes
                 for attr in ['bc_lower','bc_upper','units']:
                     attr_name = "%s.%s" % (dim_name,attr)